I think maybe the confusion is coming from the role of missionaries. Yes, I realize that ostensibly, the purpose of missionaries is to get people to believe in a certain god. I'm referring to the more political function of missionaries. The Spanish Empire funded the missions less because they wanted natives to believe in Christ or Lord God of the Bible, than because they were hoping to colonize those territories. (See the movie The Mission for how that worked.) The missionaries themselves may have believed they were working in service of Jesus Christ. But they were required to send "intelligence" of the native populations back to the court. The Conquistadors used this information to plan their conquest of the new territories. The other role of the missionaries (again - not the stated religious role, but the one that the monarchs benefited from) was to make the native population more friendly to the European invaders.